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The NCI Cancer Imaging Program organized those CPTAC specific cases as an opportunity for researchers to explore what such combined research resources might offer. They consist of 28 ovarian (TCGA-OV) and 14 breast (TCGA-BRCA) cases. Those imaging cases are easily downloadable from TCIA using the drop-down Tool-menu entry “shared lists” under the separate names of: "CPTAC BreastAnalyzed" and "CPTAC OV Analyzed". The images of those grouped cases can be down-loaded by entering the afore-mentioned “shared lists” names on https://public.cancerimagingarchive.net/ncia/searchCustomList.jsf Their individual case-matched CPTAC Proteomic Analysis Data is down-loadable from: https://cptac-data-portal.georgetown.edu/cptacPublic/ Moreover, the case specific Clinical Data that matches each of those TCIA archived image cases are attached here as XLS sheets.
An early CPTAC publication which reports on a more comprehensive collection of cases from those TCGA tumor data collections (BRCA and OV) can be found at: “Comprehensive quantitative analysis of ovarian and breast cancer tumor peptidomes”. Xu Z, et al., J Proteome Res. 2015 Jan 2;14(1):422-33. doi: 10.1021/pr500840w.
An excellent review of proteomic biomarkers is the publication: "Proteomics in cancer biomarkers discovery: challenges and applications." Sallam RM1. Dis Markers. 2015;2015:321370. doi: 10.1155/2015/321370.
CPTAC and TCGA Collections Publication Guidelines
TCIA publication guidelines, derived from the policy outlined by TCGA, must be followed in addition to the TCGA Data Portal publication policy: http://cancergenome.nih.gov/abouttcga/policies/publicationguidelines.
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